Structure of PDB 6vf3 Chain A Binding Site BS04

Receptor Information
>6vf3 Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRVD
LVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKT
FFQAASEEDIFRHLGLEYLPPEQRNA
Ligand information
Ligand ID8GT
InChIInChI=1S/C10H16N5O15P3/c11-9-13-6-3(7(18)14-9)12-10(19)15(6)8-5(17)4(16)2(28-8)1-27-32(23,24)30-33(25,26)29-31(20,21)22/h2,4-5,8,16-17H,1H2,(H,12,19)(H,23,24)(H,25,26)(H2,20,21,22)(H3,11,13,14,18)/t2-,4-,5-,8-/m1/s1
InChIKeyJCHLKIQZUXYLPW-UMMCILCDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)O)O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)O)O)O[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.341NC1=NC2=C(NC(=O)N2[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C(=O)N1
CACTVS 3.341NC1=NC2=C(NC(=O)N2[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)C(=O)N1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(N2C(=O)NC1=C2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O15 P3
Name8-OXO-GUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1230627
DrugBank
ZINCZINC000058650735
PDB chain6vf3 Chain A Residue 506 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vf3 DNA Polymerase Mu, 8-oxorGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)
Resolution1.521 Å
Binding residue
(original residue number in PDB)		G319 G320 R323 K325 H329 D330 D332 G433 W434 G436 K438
Binding residue
(residue number reindexed from 1)		G182 G183 R186 K188 H192 D193 D195 G265 W266 G268 K270
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vf3, PDBe:6vf3, PDBj:6vf3
PDBsum6vf3
PubMed
UniProtQ9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)

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